TB-Profiler result

Run: SRR13837660
Summary

Run ID: SRR13837660

Sample name:

Date: 03-04-2023 09:15:23

Number of reads: 298094

Percentage reads mapped: 96.38

Strain: lineage4.9

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.25 streptomycin
embB 4247448 p.His312Arg missense_variant 0.18 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 6703 c.-599G>C upstream_gene_variant 0.67
gyrA 7837 p.Gly179Val missense_variant 1.0
gyrA 8207 c.906T>C synonymous_variant 0.15
gyrA 8219 c.918T>C synonymous_variant 0.18
gyrA 8225 c.924T>C synonymous_variant 0.17
gyrA 8234 c.933T>C synonymous_variant 0.18
gyrA 8247 p.Ile316Val missense_variant 0.2
gyrA 8264 c.963T>C synonymous_variant 0.2
gyrA 8267 c.966G>C synonymous_variant 0.2
gyrA 8270 c.969G>C synonymous_variant 0.22
gyrA 8276 c.975G>A synonymous_variant 0.25
gyrA 8283 p.Ile328Leu missense_variant 0.25
gyrA 8288 c.987T>C synonymous_variant 0.25
gyrA 8294 c.993T>C synonymous_variant 0.25
gyrA 9224 c.1923C>T synonymous_variant 0.22
rpoB 762257 c.2451C>G synonymous_variant 1.0
rpoC 762434 c.-936T>C upstream_gene_variant 0.18
rpoC 763636 c.267T>C synonymous_variant 0.18
rpoC 764911 c.1542A>G synonymous_variant 0.18
rpoC 764932 c.1563C>A synonymous_variant 0.17
rpoC 766726 c.3357T>C synonymous_variant 0.18
rpoC 766738 c.3369G>C synonymous_variant 0.2
mmpL5 777730 p.Gly251Arg missense_variant 1.0
fbiC 1304757 c.1827A>G synonymous_variant 0.4
fbiC 1304778 c.1848T>C synonymous_variant 0.5
fbiC 1304784 c.1854T>C synonymous_variant 0.33
fbiC 1304787 c.1857T>G synonymous_variant 0.33
fbiC 1304800 c.1870C>A synonymous_variant 0.33
fbiC 1304808 c.1878C>G synonymous_variant 0.29
fbiC 1304811 c.1881C>G synonymous_variant 0.29
fbiC 1304816 p.His629Arg missense_variant 0.71
fbiC 1304829 c.1899T>C synonymous_variant 0.25
fbiC 1304832 c.1902C>T synonymous_variant 0.25
fbiC 1304869 p.Leu647Met missense_variant 1.0
tlyA 1918236 c.297A>C synonymous_variant 0.25
tlyA 1918248 c.309T>C synonymous_variant 0.22
tlyA 1918251 c.312T>G synonymous_variant 0.22
tlyA 1918258 p.His107Glu missense_variant 0.2
tlyA 1918271 p.Ala111Val missense_variant 0.18
tlyA 1918275 c.336T>C synonymous_variant 0.18
tlyA 1918278 c.339C>G synonymous_variant 0.18
tlyA 1918310 p.Asn124Ser missense_variant 0.15
tlyA 1918315 p.Pro126Ala missense_variant 0.15
tlyA 1918323 c.384G>C synonymous_variant 0.15
tlyA 1918326 c.387G>C synonymous_variant 0.15
tlyA 1918330 p.Leu131Val missense_variant 0.15
tlyA 1918346 p.Ala136Val missense_variant 0.15
tlyA 1918352 p.Gly138Asp missense_variant 0.14
tlyA 1918356 c.417C>G synonymous_variant 0.15
tlyA 1918359 c.420A>G synonymous_variant 0.17
tlyA 1918362 c.423G>C synonymous_variant 0.17
tlyA 1918527 c.588G>T synonymous_variant 1.0
ndh 2102259 p.Ser262Ala missense_variant 1.0
ndh 2102548 c.495A>G synonymous_variant 0.33
ndh 2102557 c.485delG frameshift_variant 1.0
katG 2156260 c.-149C>A upstream_gene_variant 1.0
PPE35 2169123 p.Thr497Ile missense_variant 1.0
kasA 2519122 c.1008G>C synonymous_variant 0.2
kasA 2519137 c.1023T>G synonymous_variant 0.2
kasA 2519158 c.1044C>T synonymous_variant 0.15
kasA 2519167 c.1053T>G synonymous_variant 0.21
kasA 2519173 c.1059C>G synonymous_variant 0.18
kasA 2519196 p.Thr361Ser missense_variant 0.21
kasA 2519215 c.1101C>T synonymous_variant 0.21
kasA 2519218 c.1104G>A synonymous_variant 0.21
kasA 2519221 c.1107G>C synonymous_variant 0.21
kasA 2519227 c.1113G>C synonymous_variant 0.21
kasA 2519230 c.1116C>T synonymous_variant 0.21
kasA 2519236 c.1122G>A synonymous_variant 0.2
kasA 2519239 c.1125A>C synonymous_variant 0.21
kasA 2519245 c.1131T>C synonymous_variant 0.23
Rv2752c 3066145 p.Leu16Ser missense_variant 1.0
thyX 3067693 p.Ile85Leu missense_variant 0.12
thyX 3067781 c.165C>G synonymous_variant 0.14
Rv3236c 3612326 p.Thr264Ile missense_variant 1.0
Rv3236c 3612504 p.His205Tyr missense_variant 1.0
Rv3236c 3612779 p.Leu113* stop_gained 1.0
fbiB 3640821 c.-714G>C upstream_gene_variant 1.0
rpoA 3878381 p.Leu43Met missense_variant 0.88
rpoA 3878543 c.-36G>C upstream_gene_variant 1.0
clpC1 4038923 c.1782A>G synonymous_variant 0.11
clpC1 4039022 c.1683A>G synonymous_variant 0.18
clpC1 4039064 c.1641C>T synonymous_variant 0.12
clpC1 4039142 c.1563A>G synonymous_variant 0.14
clpC1 4039145 c.1560G>C synonymous_variant 0.15
embC 4240536 c.678delC frameshift_variant 1.0
embB 4247407 c.894G>C synonymous_variant 0.18
embB 4247425 c.912G>C synonymous_variant 0.17
embB 4247434 c.921C>G synonymous_variant 0.18
embB 4247437 c.924A>G synonymous_variant 0.18
embB 4247440 c.927C>G synonymous_variant 0.18
embB 4247446 c.933C>T synonymous_variant 0.18
embB 4247464 c.951C>G synonymous_variant 0.2
embB 4247470 c.957T>C synonymous_variant 0.22
embB 4247491 c.978G>C synonymous_variant 0.22
embB 4247497 c.984T>C synonymous_variant 0.22
embB 4248562 c.2049G>C synonymous_variant 1.0